Identifies cell-to-cell Interaction Changed Genes (ICG), i.e. genes that are differentially expressed due to proximity to other cell types.#'
findInteractionChangedGenes(
gobject,
expression_values = "normalized",
selected_genes = NULL,
cluster_column,
spatial_network_name = "Delaunay_network",
minimum_unique_cells = 1,
minimum_unique_int_cells = 1,
diff_test = c("permutation", "limma", "t.test", "wilcox"),
mean_method = c("arithmic", "geometric"),
offset = 0.1,
adjust_method = c("bonferroni", "BH", "holm", "hochberg", "hommel", "BY", "fdr",
"none"),
nr_permutations = 1000,
exclude_selected_cells_from_test = T,
do_parallel = TRUE,
cores = NA,
set_seed = TRUE,
seed_number = 1234
)giotto object
expression values to use
subset of selected genes (optional)
name of column to use for cell types
name of spatial network to use
minimum number of target cells required
minimum number of interacting cells required
which differential expression test
method to use to calculate the mean
offset value to use when calculating log2 ratio
which method to adjust p-values
number of permutations if diff_test = permutation
exclude interacting cells other cells
run calculations in parallel with mclapply
number of cores to use if do_parallel = TRUE
set a seed for reproducibility
seed number
cpgObject that contains the Interaction Changed differential gene scores
Function to calculate if genes are differentially expressed in cell types when they interact (approximated by physical proximity) with other cell types. The results data.table in the cpgObject contains - at least - the following columns:
genes: All or selected list of tested genes
sel: average gene expression in the interacting cells from the target cell type
other: average gene expression in the NOT-interacting cells from the target cell type
log2fc: log2 fold-change between sel and other
diff: spatial expression difference between sel and other
p.value: associated p-value
p.adj: adjusted p-value
cell_type: target cell type
int_cell_type: interacting cell type
nr_select: number of cells for selected target cell type
int_nr_select: number of cells for interacting cell type
nr_other: number of other cells of selected target cell type
int_nr_other: number of other cells for interacting cell type
unif_int: cell-cell interaction